Innocence Lost
by AkumanoshippoNiamh
Summary: Three years of torture and experiments, three years of isolation. Danny finally breaks free but he's not the same ... he isn't Danny Phantom anymore
1. Chapter 1

**I do not own Danny Phantom (if I did there WOULD be a season 4) only this plotline. **

**So please enjoy ….**

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**Chapter 1**

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**_Insanity is doing the same thing, over and over again, but expecting different results._**

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He laid on the cold concrete, letting it soothe the new wounds left over from _their_ experiments. It didn't hurt anymore; it stopped hurting a long time ago.

Stale blood and ectoplasm could be smelt, _they _had figured out he was different, he didn't know how but _they_ did. Someone had told _them_, he couldn't remember though; his past was a complete blank, every time he tried to remember he would see an array of colors; blue, orange, teal, purple and then he would go unconscious.

Opening his eyes, the green neon giving light to dark filled room, no not a room, a room implied that there was a door, a way of getting out, there was none here. This is a cage. Bars intended to keep him locked up like the animal he was.

He longed to be outside, smell the fresh air, have the sun warm his ice-cold skin, see the blue shift from orange to twilight to complete darkness then back to orange.

It was idiotic dream to have, he would never get out of here, had long given up hope, the hope of escaping, the hope of someone, anyone, saving him, the hope of dying.

He had tried so many time that he lost count to escape. The walls had some element of ectoplasm in them, preventing him from phasing. When he did make out it of confides and make it out to the hall, he would be greeted with an army of men and charged up guns. Over and over he did it expecting it to be different each time. It never was.

C_lick_

A sudden shot of light blinded him, he shielded his eyes in a vain attempt, before when he still had hope and dignity he would have fought back, but _they _broke him, turned him into the little obedient pup _they_ wanted. Rough calloused hands grabbed his malnourished form and dragged him none too gently from his cage. This was an everyday occurrence, after the experiments they would question him, ask him about his life, how he became like he was now, if there are more like him and every time he would tell them he didn't know.

The rough hands pushed him through ever winding halls, it reminded him of a maze, halls upon halls many leading to dead ends, only one way out and then the monster stopping anyone from leaving. _They _were the monster stopping him from leaving. They stood before a steel door that glowed an eerie green. Rough hands punched in a code, and then pushed him in once the door was open.

The door shut behind him, leaving him in the bleak room. This room was different from the other ones he had been in he noted, aside from the door no green coated the walls, leaving them free for him to phase through them, a one way window occupied the wall opposite him, there were no cameras, a simple plain wooden table sat in the middle of the floor, chairs on each side.

"Please do sit down." He looked up to see a man no older than thirty with a balding head, black sleek shades covered his eyes, his face was thin as were his lips, a scar started from the corner of his eye and made it's way down to his lips. He wore the usual white suit but unlike the others that he had seen medals adorned the left side of his chest. How had he not noticed him?

"That doesn't look comfortable, standing there, please I insist do have a seat." The man had a strange tone in his voice, the smile it was fake. He didn't trust the man in front of him but then he never trusted anyone.

The man's smile faltered before he regained his composure, giving a small sigh he sat down in one of the chairs, clasped his hands and looked dead straight into his eyes. This was also different, normally _they_ would force him to sit down, strap with restraints, an ectogun against his temple.

"Now, I'm going to ask a few questions and answer with yes or no … Do you understand?" The strange tone left the man's voice being replaced with a cold edge that he was accustomed to.

He nodded. The man raised an eyebrow at him but continued on.

"Is your ID number 05315dp?"

He nodded again.

"You have been here for three years?"

Another nod.

"Your room number is 490?"

And so it went on, question after question and he answered each and every one. They were simple enough to answer; none of them required him to think about his past. He started to relax slightly, evening choosing to shift his weight on to his left foot and lean against the wall.

"Do you know a place called Amity Park?"

He straightened up from his relaxed position, he knew this question not the but the question itself. _They _would ask it when he least expect it, thinking he would slip up but he truly didn't know the answer, _they _thought he was lying. He shook his head.

He saw the man's eye twitch faintly but the man opted to say nothing and moved onto the next question.

"Did you ever attend a school named Casper High?"

He shook his now aching head. The colours started to flash behind his eyes. But that was nothing compared to what happened next.

"Do you know the name Daniel Fenton?"

Pure white pain flashed through his skull, done his spine making him fall to his knees. He reached out with his hands and gripped his once snow white hair in a vain attempt to soothe the pain, he hated it, this weakness, it was mental, he couldn't do anything about but suffer. He felt like laughing at the last thought, three years of experiments, torture, starvation, isolation, the list went on, a headache should be a gentle pat on the back. Black spots started to cover his vision; he welcomed the black waters that would surely follow soon. Complete and utter darkness just like the night sky, he would imagine the stars

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Agent H glanced at the writhing teen on the ground in front of him and gave a smile. This specimen was truly a scientific marvel. Both dead and alive although some in the GiW would argue that he was more dead than alive right now. When they were told by some very trustworthy sources that this so called ghost was half human they didn't believe them, instead they laugh in their faces. But when they made the first incision for the vivisection and saw blood mixed in with ectoplasm pour out … well they were amazed to say at the least.

A Halfa, half human, half ghost. He had all of the powers of a ghost yet experienced all the emotions of a human including pain. And that's what they used to break him down piece by piece; torture. However he lost his mind as a result, halting their process in finding out about any other hybrid like him.

It happened every time he was questioned, they would start off with some easy questions then move onto the more personal ones but the result was always the same. He would lose it, go unconscious or in some extreme cases go on a rampage and would have to be restrained.

He pressed his communicator hidden in his ear, "Test 812 … results … standard questions answered … personal question failed."

Agent H got up gave one last glance at the adolescent who had now gone deathly still and walked out. This cast was certainly a challenge, a difficult one but Agent H loved challenges in fact he was a master at them.

Danny Phantom would be the most complicated challenges he would ever face.

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**_A.N ~ Reviews are always appreciated _**


	2. Chapter 2

**I do not own Danny Phantom (if I did there WOULD be a season 4) only this plotline. **

**So please enjoy ….**

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**Chapter 2**

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_**Insanity is doing the same thing, over and over again, but expecting different results.**_

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Three years it has been, three years Amity Park had been left unprotected. Three years since Daniel James Fenton died. Everyone believed it to be the result of a ghost attack. The boy's parents whose profession was to hunt and experiment on ghosts, blamed the town's hero; Danny Phantom. At first no one believed them, how could a ghost who dedicated his afterlife to protecting Amity, just kill an innocence boy for no apparent reason, however when the ghost boy disappeared and pictures were released from an unknown source showing the white haired ghost attacking Danny Fenton, it changed their minds.

No one saved for a few knew that both Danny Fenton and Danny Phantom were the same.

One of these few was Vlad Masters, billionaire, mayor of Amity Park and half ghost. When the boy's body was discovered after a month of missing, he knew something was amiss. Though the body looked like that of his little badger's, something told him that it wasn't. He kept quite however, choosing to do his own investigation. Except every lead was a dead end, he questioned every ghost he knew personally, checked every government file he could get his hands on, but it was always the same result; nothing. He even went to Clockwork but the time ghost gave no information just an encrypted 'Everything is as it should be.'

He gave up eventually and instead dedicated his life to his study. That was why he was in the facility known as GiW, rumor had it that they had captured a scientific marvel that blew away all they're years of research,

He was currently talking to one of the lead scientist, a scrawny man perhaps mid forties with shaggy brown hair, glasses covered his dull hazel eyes. He hadn't stopped wriggling his hands since he had met with Vlad.

"Well … you see Mr. Masters the problem is … this research is for private personal only."

Vlad gave a tight lipped smile. "I understand the situation, but I must remind you that I am one if not the only main sponsor of this organization, and as a result I demand full access to anything that this facility has to offer." The billionaire had to restrain himself from shouting towards the end.

The shriveling scientist began to sweat under the intense glare of the billionaire. "I also understand but without the permission of my superior, I can no-"

"- Then bring me to your superior." The hybrids eyes flashed a dangerous red, thankfully the scientist didn't notice. Said scientist shifted his gaze to the white tiled floor.

"Ah … well you see he is currently busy right now…" Vlad was seriously considering overshadowing this pathetic scientist and throwing him repeatedly against the wall. He had been arguing with this blubbering buffoon the minute he stepped into the building. All he wanted was a few simple answers to a few simple questions. He was about to leave, when a door which he hadn't notice slide open revealing a man dressed in the usual GiW outfit, the hybrid instantly noticed a scar coming from the corner of his right eye and traveling down to his thin lips.

"Is there a problem here, Dr. Elric?" His voice was smooth and deep. He glanced to Vlad then back to the scientist.

"No sir … I … I was just kindly directing Mr. Masters out." The scientist now identified as Dr, Elric stuttered. He seemed more nervous around the newcomer then he was around Vlad.

"Mr. Masters you say?" Vlad looked from the scientist towards the man. He could sense something not right about him. "Let me introduce myself, I am Agent H, Superior Officer … It's a pleasure to meet you." Agent H took off his shades, letting Vlad see that the Agent was blind in his right eye.

"Like wise and please call me Vlad."

"Well Vlad is there a reason why you are here, if you don't mind me asking."

Vlad didn't like the smooth talking voice of this Guys in White agent; it almost made the billionaire sick to his stomach. Before he could answer, the once forgotten Dr. Elric spoke up.

"He wanted information on Project 416."

Agent H raised an eyebrow at the nervous scientist. "I see … and was there was a problem that you could not show him?"

"N… no sir … there was not."

"You are dismissed Dr. Elric."

"Yes sir" Dr. Elric gave a curt nod before scurrying down the white hall and out of sight. Agent H turned to face Vlad once more.

"Sorry about that, I'm sure your used to though Vladdie" Vlad was startled when the man clasped the hybrid on the shoulder as if they were old friends and not strangers who only met a mere few minutes ago.

"Shall we discus, Project 416?"

Vlad gave a nod. "We shall."

The hybrid never noticed the small specks of ecto and blood on the floor leading into the room.

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_**A.N ~ Reviews are always appreciated **_

_**P.S If anyone guess where I got the name Elric gets a cookie xD **_


	3. Chapter 3

**I do not own Danny Phantom (if I did there WOULD be a season 4) only this plot line. **

**So please enjoy ….**

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**Chapter 3  
**

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_**Insanity is doing the same thing, over and over again, but expecting different results.**_

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Intense pain that was the first thing he felt when he woke up. It pulsated in his head, not allowing him to think clearly. Dazed, he stood up from his fetal position on the ground. Glancing around him, he noticed that he was back in his confined cell. He had no memory of returning here. He must have had another episode. He hoped their use for him would run out soon, surely after so long they would find what they were looking for and they would let him free. But if that did happen, and he was set free, where would he go? He had no idea what the outside world was like, he had only seen glimpses of it and that was when his training required wide open spaces. He heard the agents talk of this place called a 'home' with these things called a 'family' living there. Everyone one of them seemed to have one, so maybe he had one, however that was unlikely considering the fact he didn't even have a name … well that was a lie his name was Project 416 or as the agents liked to call him 'freak'. At least it's better than nothing, right?

No. It wasn't better, he wanted a proper name. He wanted this 'home' place and 'family' thing.

He would ask next time, if they were nearly done. It would surprise them taking into account he had no memory of ever talking to them aside from the screaming but that couldn't be considered as talking. Yes, he would ask, he been here since he could remember, certainly he deserved some answers to the many questions that swirled around his head.

Letting a small smile etch its way onto his face at the thought as he slowly made his way over to one of the corners of his square domain. Sliding down the cold stone wall he was met with an equally cold floor. He brought his knees to meet with his chest and wrapped his hands around them, hopping the new position would offer some form of warmth. The pain on his head had subsided some what. He had just started to examine the grime and dried blood under his fingernails when he heard the tell tale sign of a door creaking. Out of instinct he pushed himself further into the corner, letting the darkness obscure him from the light of the hallway.

"-As you can see Mr. Masters, from our recent discoveries, we can build a new type of human, a better model or upgrade if you will."

"Interesting … I must ask Agent H, where did you get such an idea?"

The young teen recognized the first voice as Agent H from the interrogation room, the one who spoke calmly and with fake concern. The second voice, the one Agent H had called Mr. Masters, was unfamiliar to him although he felt as if he should know it. Both men walked into the stone cell, blocking what little light came from the hall. He noticed that the agent was taller than he first thought when compared to the man beside him, who could not look more out of place. Said man wore a black suit with a red tie and handkerchief stuffed neatly into breast pocket and had his greying hair tied back in a ponytail which looked odd to the white haired teen. The only people he had seen with long hair was the occasional female scientist or agent.

"This specimen right here Vlad, is the reason for such an idea." The so called experiment glanced to the GiW agent before settling his gaze back on the billionaire. "_It _is known as a halfa … half ghost half human." The boy looked back the agent, he had never heard them call him a halfa before but then he didn't really know what he was.

"I see." The man; Vlad mused. The man eyed the 'specimen' however he could not make out the features but from it's figure he could see that it was male built but unnaturally thin. Peeking out from the darkness he saw two white boots. His eyes widened in astonishment and horror but he quickly wiped the expression from his face. No, this couldn't be his little badger.

"Amazing, is it?" The older hybrid was brought out of his revelation to the almost maniac smile of Agent H. He resisted the murderous urge rising in him and instead gave a tight smile.

"It is, and answer me this … where did you find such a creature Agent H?" Vlad unknowingly positioned he body in front of the younger hybrid in a protective manner.

"Ah, Vlad I can't go telling all my secrets, now can I?" The agent waved his finger as if he were scolding a bold child. The billionaire felt his eye twitch slightly.

"Then may I have a moment alone with the subject and please don't worry about my safety, I deal with this kind of matter all the time." Vlad gave what he hoped was a convincing smile.

The agent clapped the man hard on the shoulder. "I see no problem in that … you have five minutes starting now." Agent H gave another smile, spun around on his heel and left the room, closing the door behind him.

Vlad gave hesitant step towards the younger halfa. The teen having watched the whole conversation take place, tensed at the approaching man. He did not seem like a threat but the white haired adolescent knew better then to judge a book by its cover. He had sensed something corrupt inside the man, though it was not as nearly as corrupt as what he sensed in the agents. The man was no more than a foot before him. He tensed even further when the grey haired man bent down and stretched out his hand as if the boy were some rabid dog backed into a corner. He opened his mouth as if were going to say something but no sound came out. It was hours or at least that was what it felt like to both hybrids before the elder of the two spoke.

"Little Badger."

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**I'm way too tired to prof read the story so I'll do it tomorrow sorry for any spelling mistakes or grammar errors, I'll make sure to fix it.**

_**To any who guessed Fullmetal Alchemist, well done. Give yourselves a pat on the back and here's your ghost cookies, made with a 100% ecto goodness (*side effects may include the ability to transform into a ghost, white hair, tanned skin, a hero complex and your own theme song.)**_

_**Thanks to whoever reviewed, they all mean so much to me**_

_**A.N ~ Reviews are always appreciated **_


	4. Chapter 4

** I do not own Danny Phantom (if I did there WOULD be a season 4) only this plotline. **

**So please enjoy ….**

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**Chapter 4**

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**_Insanity is doing the same thing, over and over again, but expecting different results._**

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_Previously on Innocence Lost …_

_He tensed even further when the grey haired man bent down and stretched out his hand as if the boy were some rabid dog backed into a corner. He opened his mouth as if were going to say something but no sound came out. It was hours or at least that was what it felt like to both hybrids before the elder of the two spoke._

_"Little Badger."_

Danny shot up from his place on the floor and growled at the man, warning him not to come any closer. Vlad for his part looked astonished at the white haired teen, even though he knew boy didn't exactly like him, what with him trying to kill his father and marry his mother. Still he couldn't understand why Daniel was acting so aggressive towards him, surely his little badger would be happy, if not ecstatic at seeing him, not cowering in a corner and growling defensively.

Vlad reached out again for the feral teen. "Little badger I'm not going to hurt you." The younger hybrid narrowed his eyes in suspicion at the man's words. He had heard them many times before, when the agents would mock him by telling him that they would let him go if he came peacefully with them, his naïve mind believed them and he ended up strapped on to steel table, his body being cut open like he was a slab of meat.

Danny saw something flash in the man's eyes but it was gone before he could see what it was. "Oh Daniel, what did they do to you?" the question sounded like if it wasn't meant for him to hear. Vlad looked towards Daniel again, noticing how gaunt the teen's features were. The boy had always been thin, but this was unnatural. Vlad could see ribs through the torn and bloody HAZMAT suit, dark circles held a permanent residence underneath the once bright neon green eyes; the white hair held none of its vividness and instead looked dirty and grey.

What had_ they_ done to him?

Danny felt uncomfortable under the elder hybrids scrutinizing gaze. He shifted slightly from one foot to the another but went tense when he felt a warm hand on his shoulder, he looked up to meet the determined midnight blue eyes. He wanted to get away from the strange man; the bad feeling in his stomach hadn't left him since he stepped into the room.

"I _will _get you out of here Daniel, do you hear me." The young hybrid was confused by the elder's words. _'Get out of here'_. He had never heard those words in that order before. He was lying, he had to be. There was no hope of getting out, ever. The billionaire sighed; he stood up and gave a sorrow filled glance to his broken little badger. He checked his watch and saw that his five minutes were nearly up; giving one last look he slowly made his way towards the door.

"There's never a way out." Vlad froze at the soft murmur, turning around he saw neon green eyes staring into his own. They held the look of defeat and desperation, so different to the mirth and over cockiness that he was used to seeing. "So … many … times." The greens turned dazed, as if the young boy was reliving a dream, no not a dream, a nightmare.

"I … I just want to see the stars." Vlad felt his heart breaking, the boy always had a fascination with astronomy, he even wanted to become an astronaut although that was unlikely due to his grades. "You're not like … _them_." The elder hybrid eyes widened in shock by the malice that dripped from the young teen's words.

"You're different from _them_." Danny gaze wondered to the floor yet again. "But you won't help … no one does." The young hybrid lifted his gaze back up to Vlad's. "Maybe I'll wake up and this will all just be a nightmare." Seeing his little badger so hopeless nearly tore Vlad apart, forgetting about his time limit, he went to the boy he so longed to be his own son.

Gently placing both his hands on the boy's thin shoulders, he made sure that Danny was focused on him before he spoke. "Like I said it before Daniel, I will get you out of here… so help me God." If Vlad wasn't the rational thinking man he was well known as, he would have snatched up the young white haired and bring him far away from this hellhole of a government organization.

"What … who … am I?" Confused green eyes stared into sad midnight blue ones. Vlad understood now, why Danny acted so aggressive towards at the start, he had forgotten who he was and doing so forgotten who Vlad was. Hopefully the memories could be retrieved, hopefully.

Vlad opened his mouth to reply but the door sliding open stopped. Looking up, he saw Agent H standing in the door, arms crossed in a casual way. The billionaire noticed the GiW agent staring at where his hands where, he realized that his hands where still on the teen's shoulders. He quickly took his hands away from the thin shoulders, straightened his tie before leaving them to rest at his side.

"I hope _it _didn't cause too much trouble." The agent let a smirk settle on his face as he stared down at the broken white haired teen that backed into the corner, he never saw Vlad tightening his hands into fists. The billionaire watched as Agent H walked towards Daniel, like a predator would stalk it's injured prey, knowing full well it had no where to run. Danny for his part stared at the advancing agent; he was scared, but for some reason didn't want to show it in front of the _'non-agent'_. H reached his target, lifting up a white gloved he gently stroked the young hybrid's cheek, moving the disheveled hair out of the way, almost like he was the boy's father.

"Such an interesting specimen… don't you think Vlad?" He glanced away from Danny to look at Vlad's expressionless gaze before returning it back to his trapped prey. Danny was even more scared and confused, he didn't like this man touching him, he preferred if he hit him, at least that physical was familiar to him. The agent smiled that overly sick nice smile he used in the interrogation room as he patted his like he was a domestic dog.

Vlad gave a loud cough, drawing the attention of the agent. He was growing queasy of the sight before him. "I do _hate _to interrupt, but as I'm sure you well know I have a time schedule to keep and I must be going."

"Ah, I understand… please let me escort you out, this place can seem like a maze to those who do not know it." Giving Danny one last pet on the head, he walked out of the cell, Vlad accompanying him.

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_"I _will _get you out of here Daniel, do you hear me" _

Agent H played the video recording tape again for what seemed like the hundredth time.

_"There's never a way out." _Came the broken reply.

According to the files on Phantom, the hybrid had refused to speak after the first year or so of being here. The scientists said _it _lost _it's _voice permanently due to all the screaming and yelling _it_ did, however this audio taped proved that statement wrong.

_"Like I said it before Daniel, I will get you out of here… so help me God."_

So, Vlad Masters, self made billionaire, world rewound business man and one of the main suppliers of anti-ghost technology knew Phantom, a freak. But how was the question. Maybe he was relative of the hybrid, a cousin or uncle maybe, no the way he acted around the specimen was to personally and protective and then there was that nickname 'Little Badger'. The type of nickname you'd give to your… child. Agent H eyes widened in shock, that couldn't be possible. _It_ was half ghost, half human… unless Vlad _was _the father and the mother was a ghost, that would explain why _it _was able to change _it's _form from human to ghost. But is that even possible?

Agent H shook his head, he had to think about this straight on. If his memory served him right Vlad Master's was one of the lead sponsors for the search for Fenton, Phantom's human alias, and it was because of Vlad that they had to come up with the fake body. But Phantom was raised by the Fentons, a family of well known ghost hunters, surely that would cause some troubles, however Masters was a close friend of the family, maybe he left Phantom there for protection, There were ghosts that wanted to hunt down Phantom, one even wanted to skin the hybrid and hang his pelt upon his walls.

Shaking the disturbing image from his head, Agent H pressed the intercom. "Agent O."

_"Yes, Sir?"_

"Move Phantom, to the solitary confinement cell on the basement floor, we might be expecting some company soon."

_"Sir yes Sir."_

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**_A.N ~ Reviews are always appreciated and if anyone has any questions please be free to ask. To anyone who reviewed, followed or favourite, hell even looked at the title... THANKS, ILOVE YOU GUYS SOOOO MUCH. Sorry for any grammar mistakes or spellings. _**


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